Automatic annotation of bioinformatics workflows with biomedical ontologies

Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community. This paper presents an approach to annotating workflows and their subcomponents with ontology terms, in an attempt to describe these artifacts in a structured way. Despite a dearth of even textual descriptions, we automatically annotated 530 myExperiment bioinformatics-related workflows, including more than 2600 workflow-associated services, with relevant ontological terms. Quantitative evaluation of the Information Content of these terms suggests that, in cases where annotation was possible at all, the annotation quality was comparable to manually curated bioinformatics resources.Comment: 6th International Symposium on Leveraging Applications (ISoLA 2014 conference), 15 pages, 4 figure

weSPOT: a cloud-based approach for personal and social inquiry

Scientific inquiry is at the core of the curricula of schools and universities across Europe. weSPOT is a new European initiative proposing a cloud-based approach for personal and social inquiry. weSPOT aims at enabling students to create their mashups out of cloud-based tools in order to perform scientific investigations. Students will also be able to share their inquiry accomplishments in social networks and receive feedback from the learning environment and their peers

weSPOT: A personal and social approach to inquiry-based learning

weSPOT is a new European initiative proposing a novel approach for personal and social inquiry-based learning in secondary and higher education. weSPOT aims at enabling students to create their mash-ups out of cloud based tools and services in order to perform scientific investigations. Students will also be able to share their inquiry accomplishments in social networks and receive feedback from the learning environment and their peers. This paper presents the research framework of the weSPOT project, as well as the initial inquiry-based learning scenarios that will be piloted by the project in real-life educational settings

Embracing Automation: Boosting Productivity and Efficiency in the Tech Sector

Project Work presented as the partial requirement for obtaining a Master's degree in Information Management, specialization in Knowledge Management and Business IntelligenceThis project explores the implementation of process automation within a tech company to streamline and optimize the Sev ABC Rota process, which involves the manual handling of critical support tickets. The current manual system poses challenges such as data entry errors, time consumption, and delays in system updates, necessitating the urgent need for automation. Power Automate, along with connectors like Excel, Outlook, Teams, and SharePoint, is utilized to automate the Sev ABC Rota process. The automation includes creating and updating data in a SharePoint list, removing engineers from the daily queue, sending email notifications, and creating a Teams group chat. The choice of Power Automate is based on its no-code functionality and compatibility with Microsoft connectors, ensuring simplicity, time savings, and increased productivity. The paper discusses the benefits and challenges of process automation and automated workflows, emphasizing their impact on productivity, cost reduction, accuracy, and customer satisfaction. Various metrics and assessment techniques, including cycle time, throughput, error rates, cost savings, and customer satisfaction, are proposed to evaluate the effectiveness of automated workflows. Additionally, emerging trends in automation, such as the combination of cognitive technologies, adoption of intelligent automation, cloud computing, and low code/no-code platforms, are discussed. The importance of change management and employee engagement in successful automation implementation is highlighted, emphasizing the need for a culture of ongoing learning and collaboration. Overall, this paper provides insights into the implementation and evaluation of process automation in the tech industry, offering a roadmap for organizations seeking to enhance efficiency and optimize operations

Bioinformatic Workflows for Generating Complete Plastid Genome Sequences - An Example from Cabomba (Cabombaceae) in the Context of the Phylogenomic Analysis of the Water-Lily Clade

The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used. Here, we present the procedure and results of sequencing, assembling, annotating and quality-checking of three complete plastid genomes of the aquatic plant genus Cabomba as well as subsequent gene alignment and phylogenetic tree inference. We accompany our findings by a detailed description of the bioinformatic workflow employed. Importantly, we share a total of eleven software scripts for each of these bioinformatic processes, enabling other researchers to evaluate and replicate our analyses step by step. The results of our analyses illustrate that the plastid genomes of Cabomba are highly conserved in both structure and gene content

Predicting Operators Fatigue in a Human in the AI Loop for Defect Detection in Manufacturing

Quality inspection, typically performed manually by workers in the past, is now rapidly switching to automated solutions, using artificial intelligence (AI)-driven methods. This elevates the job function of the quality inspection team from the physical inspection tasks to tasks related to managing workflows in synergy with AI agents, for example, interpreting inspection outcomes or labeling inspection image data for the AI models. In this context, we have studied how defect inspection can be enhanced, providing defect hints to the operator to ease defect identification. Furthermore, we developed machine learning models to recognize and predict operators’ fatigue. By doing so, we can proactively take mitigation actions to enhance the workers’ well-being and ensure the highest defect inspection quality standards. We consider such processes to empower human and non-human actors in manufacturing and the sociotechnical production system. The paper first outlines the conceptual approach for integrating the operator in the AI-driven quality inspection process while implementing a fatigue monitoring system to enhance work conditions. Furthermore, it describes how this was implemented by leveraging data and experiments performed for a real-world manufacturing use case

The case for cloud service trustmarks and assurance-as-a-service

Cloud computing represents a significant economic opportunity for Europe. However, this growth is threatened by adoption barriers largely related to trust. This position paper examines trust and confidence issues in cloud computing and advances a case for addressing them through the implementation of a novel trustmark scheme for cloud service providers. The proposed trustmark would be both active and dynamic featuring multi-modal information about the performance of the underlying cloud service. The trustmarks would be informed by live performance data from the cloud service provider, or ideally an independent third-party accountability and assurance service that would communicate up-to-date information relating to service performance and dependability. By combining assurance measures with a remediation scheme, cloud service providers could both signal dependability to customers and the wider marketplace and provide customers, auditors and regulators with a mechanism for determining accountability in the event of failure or non-compliance. As a result, the trustmarks would convey to consumers of cloud services and other stakeholders that strong assurance and accountability measures are in place for the service in question and thereby address trust and confidence issues in cloud computing

Document Automation Architectures: Updated Survey in Light of Large Language Models

This paper surveys the current state of the art in document automation (DA). The objective of DA is to reduce the manual effort during the generation of documents by automatically creating and integrating input from different sources and assembling documents conforming to defined templates. There have been reviews of commercial solutions of DA, particularly in the legal domain, but to date there has been no comprehensive review of the academic research on DA architectures and technologies. The current survey of DA reviews the academic literature and provides a clearer definition and characterization of DA and its features, identifies state-of-the-art DA architectures and technologies in academic research, and provides ideas that can lead to new research opportunities within the DA field in light of recent advances in generative AI and large language models.Comment: The current paper is the updated version of an earlier survey on document automation [Ahmadi Achachlouei et al. 2021]. Updates in the current paper are as follows: We shortened almost all sections to reduce the size of the main paper (without references) from 28 pages to 10 pages, added a review of selected papers on large language models, removed certain sections and most of diagrams. arXiv admin note: substantial text overlap with arXiv:2109.1160

Game-like interactive environment using BIM-Based Virtual Reality for the Timber Frame Self-Build Housing Sector

BIM, gamification, and Virtual Reality applications are more often used to serve the interests of Design for Manufacture and Assembly (DfMA). This paper presents a comprehensive study to exploit these technologies’ innovative approaches and capabilities. The study is specifically adopted to implement small and medium-size architectural and construction practices with a limited budget and time dedicated to visualisation creation. The collected evidence proved that a game-like platform combined with BIM could provide simplified data delivery to a client, leading to customer satisfaction, confidence and increased sales. The designed workflow and templates were tested in the case study of a small self-build construction company. The staff was trained to provide BIM data correctly and use supplied game templates. The case study demonstrated that automation of the VR House Configurator creation is achievable. The study’s outcome is an integrated solution to regenerate BIM models in the game environment and utilise the house configurator’s organised furniture library and costing interface. Furthermore, the usability tests confirmed the applicability, practicability, and validity of the developed framework and tools to deal with the revealed challenges in the self-build sector. Finally, the research provided a fresh approach for the companies in the sector, a step-by-step guide for implementing the innovative changes, and detailed descriptions of the methodologies and workflows